I always followed http://cran.r-project.org/bin/linux/ubuntu/ to install R on Ubuntu 8.1. I had no errors before! > install.packages("XML") Warning in install.packages("XML") : argument 'lib' is missing: using '/usr/local/lib/R/site-library' --- Please select a CRAN mirror for use in this session --- Loading Tcl/Tk interface ... done trying URL 'http://cran.fhcrc.org/src/contrib/XML_1.98-1.tar.gz' Content type 'application/x-gzip' length 648274 bytes (633 Kb) opened URL ================================================== downloaded 633 Kb * Installing *source* package 'XML' ... checking for gcc... gcc checking for C compiler default output file name... a.out checking whether the C compiler works... yes checking whether we are cross compiling... no checking for suffix of executables... checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ANSI C... none needed checking how to run the C preprocessor... gcc -E checking for sed... /bin/sed checking for xml2-config... no Cannot find xml2-config ERROR: configuration failed for package 'XML' ** Removing '/usr/local/lib/R/site-library/XML' The downloaded packages are in /tmp/RtmpqCLrkQ/downloaded_packages Warning message: In install.packages("XML") : installation of package 'XML' had non-zero exit status > On Mon, Dec 1, 2008 at 1:42 PM, Hervé Pagès <hpages@fhcrc.org> wrote: > Hi Tiandao, > > What OS do you have? How did you install R? It looks like you cannot > install an R package with native code at all. Please try > > > install.packages("XML") > > and show us the complete output. > You could also try the R-help mailing list (r-help@r-project.org) > since your problem doesn't seem to be Bioconductor-specific. > > Cheers, > H. > > > Tiandao Li wrote: > >> Hello, >> >> I tried to install BioC 2.3 on a new laptop (HP AMD Turion x2). However I >> constantly had the following warnings, I tried several times for the last >> few days. I never had this kind of errors before. >> >> sudo R >> >> source("http://bioconductor.org/biocLite.R") >>> >> >> biocLite() >>> >> >> warnings() >>> >> Warning messages: >> 1: In install.packages(pkgs = pkgs, repos = repos, dependencies = >> dependencies, ... : >> installation of package 'Matrix' had non-zero exit status >> 2: In install.packages(pkgs = pkgs, repos = repos, dependencies = >> dependencies, ... : >> installation of package 'preprocessCore' had non-zero exit status >> 3: In install.packages(pkgs = pkgs, repos = repos, dependencies = >> dependencies, ... : >> installation of package 'IRanges' had non-zero exit status >> 4: In install.packages(pkgs = pkgs, repos = repos, dependencies = >> dependencies, ... : >> installation of package 'affy' had non-zero exit status >> 5: In install.packages(pkgs = pkgs, repos = repos, dependencies = >> dependencies, ... : >> installation of package 'affydata' had non-zero exit status >> 6: In install.packages(pkgs = pkgs, repos = repos, dependencies = >> dependencies, ... : >> installation of package 'Biostrings' had non-zero exit status >> 7: In install.packages(pkgs = pkgs, repos = repos, dependencies = >> dependencies, ... : >> installation of package 'matchprobes' had non-zero exit status >> 8: In install.packages(pkgs = pkgs, repos = repos, dependencies = >> dependencies, ... : >> installation of package 'vsn' had non-zero exit status >> 9: In install.packages(pkgs = pkgs, repos = repos, dependencies = >> dependencies, ... : >> installation of package 'gcrma' had non-zero exit status >> 10: In install.packages(pkgs = pkgs, repos = repos, dependencies = >> dependencies, ... : >> installation of package 'simpleaffy' had non-zero exit status >> 11: In install.packages(pkgs = pkgs, repos = repos, dependencies = >> dependencies, ... : >> installation of package 'affyPLM' had non-zero exit status >> 12: In install.packages(pkgs = pkgs, repos = repos, dependencies = >> dependencies, ... : >> installation of package 'affyQCReport' had non-zero exit status >> >> sessionInfo() >>> >> R version 2.8.0 (2008-10-20) >> i486-pc-linux-gnu >> >> locale: >> >> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en _US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;L C_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDE NTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> loaded via a namespace (and not attached): >> [1] tcltk_2.8.0 tools_2.8.0 >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > -- > Hervé Pagès > > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M2-B876 > P.O. Box 19024 > Seattle, WA 98109-1024 > > E-mail: hpages@fhcrc.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 > [[alternative HTML version deleted]]